.command.sh - Workdir - NFCORE_SAREK:SAREK:CRAM_SAMPLE_INTEGRITY:CRAM_QC_RECAL:SAMTOOLS_STATS (1136_5Z2-T1-TDNA-1_A23MYM7LT4_11)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/05/d0f39d368982e64d4a88b467a484a6/.command.sh
Size: 427 bytes
Task: NFCORE_SAREK:SAREK:CRAM_SAMPLE_INTEGRITY:CRAM_QC_RECAL:SAMTOOLS_STATS (1136_5Z2-T1-TDNA-1_A23MYM7LT4_11)
Attempt

Content

#!/bin/bash -Ceuo pipefail
samtools \
    stats \
    --threads 2 \
    --reference Homo_sapiens_assembly38.fasta \
    1136_5Z2-T1-TDNA-1_A23MYM7LT4_11.recalibrated.bam \
    > 1136_5Z2-T1-TDNA-1_A23MYM7LT4_11.stats

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:CRAM_SAMPLE_INTEGRITY:CRAM_QC_RECAL:SAMTOOLS_STATS":
    samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')
END_VERSIONS